Silica Microcapsules for Long-Term, Robust, and Reliable Room Temperature RNA Preservation

Covalent Organic Frameworks as Nano-Reservoir for Room Temperature RNA Storage

The emerging role of Ribonucleic acids (RNAs) as therapeutics is alluring. However, RNAs are extremely labile under ambient conditions and typically need to be stored in cryogenic conditions (-20 °C to -80 °C). Hence, storage, stabilization, and transportation of RNA under ambient conditions have been an arduous task and remain an unsolved problem. In this work, a guanidinium-based ionic covalent organic framework (COF), TTGCl with nanotubular morphology, was synthesized and used as nano-reservoirs for room-temperature storage of RNA. To understand the role of the nanotubular morphology and chemical nature of TTGCl in stabilizing the RNA structure and for comparison purposes, a neutral COF, TMT-TT, is synthesized and studied. Further, density functional theory (DFT) studies confirmed non-covalent interaction between the COFs and the RNA nucleobases, facilitating reversible storage of RNA. RNA loaded in COFs was found to be resistant to enzymatic degradation when treated with RNase. Gel electrophoresis and sequencing confirmed the structural integrity of the recovered RNAs and their further processibility.

Long-term whole blood DNA preservation by cost-efficient cryosilicification

Deoxyribonucleic acid (DNA) is the blueprint of life, and cost-effective methods for its long-term storage could have many potential benefits to society. Here we present the method of in situ cryosilicification of whole blood cells, which allows long-term preservation of DNA. Importantly, our straightforward approach is inexpensive, reliable, and yields cryosilicified samples that fulfill the essential criteria for safe, long-term DNA preservation, namely robustness against external stressors, such as radical oxygen species or ultraviolet radiation, and long-term stability in humid conditions at elevated temperatures. Our approach could enable the room temperature storage of genomic information in book-size format for more than one thousand years (thermally equivalent), costing only 0.5 $/person. Additionally, our demonstration of 3D-printed DNA banking artefacts, could potentially allow 'artificial fossilization'.

Simple and Economical Extraction of Viral RNA and Storage at Ambient Temperature

RNA extraction is essential for the molecular detection of common viral pathogens. However, available extraction methods and the need for ultra-cold storage limit molecular testing in resource-constrained settings. Herein, we describe the development of an economical RNAExtraction and Storage (RNAES) protocol that eliminates requirements for instrumentation, expensive materials, and preserved cold chain. Through an iterative process, we optimized viral lysis and RNA binding to and elution from glass fiber membranes included in simple RNAES packets. Efficient viral lysis was achieved with a nontoxic buffer containing sucrose, KCl, proteinase K, and carrier RNA. Viral RNA binding to glass fiber membranes was concentration dependent across seven orders of magnitude (4.0–10.0 log₁₀ copies/μL) and significantly increased with an acidic arginine binding buffer. For the clinical evaluation, 36 dengue virus (DENV)-positive serum samples were extracted in duplicate with the optimized RNAES protocol and once in an EMAG instrument (bioMérieux). DENV RNA was successfully extracted from 71/72 replicates (98.6%) in the RNAES protocol, and real-time RT-PCR cycle threshold (C_T) values correlated between extraction methods. DENV RNA, extracted from clinical samples, was stable when stored on dried RNAES membranes at ambient temperature for up to 35 days, with median eluate RNA concentration decreasing by 0.18 and 0.29 log₁₀ copies/μL between day 0 and days 7 and 35, respectively. At a cost of $0.08/sample, RNAES packets address key limitations to available protocols and may increase capacity for molecular detection of RNA viruses.

IMPORTANCE RNA extraction methods and ultra-cold storage requirements limit molecular testing for common viruses. We developed a simple, flexible, and economical method that simultaneously addresses these limitations. At $0.08/sample, the new RNAExtraction and Storage (RNAES) protocol successfully extracted viral RNA from acute-phase sera and provided stable, ambient-temperature RNA storage for 35 days. Using this approach, we expect to improve RNA virus detection and outbreak response in resource-constrained settings.

Design considerations for advancing data storage with synthetic DNA for long-term archiving

Deoxyribonucleic acid (DNA) is increasingly emerging as a serious medium for long-term archival data storage because of its remarkable high-capacity, high-storage-density characteristics and its lasting ability to store data for thousands of years. Various encoding algorithms are generally required to store digital information in DNA and to maintain data integrity. Indeed, since DNA is the information carrier, its performance under different processing and storage conditions significantly impacts the capabilities of the data storage system. Therefore, the design of a DNA storage system must meet specific design considerations to be less error-prone, robust and reliable. In this work, we summarize the general processes and technologies employed when using synthetic DNA as a storage medium. We also share the design considerations for sustainable engineering to include viability. We expect this work to provide insight into how sustainable design can be used to develop an efficient and robust synthetic DNA-based storage system for long-term archiving.

Integrating DNA Encapsulates and Digital Microfluidics for Automated Data Storage in DNA

Using DNA as a durable, high-density storage medium with eternal format relevance can address a future data storage deficiency. The proposed storage format incorporates dehydrated particle spots on glass, at a theoretical capacity of more than 20 TB per spot, which can be efficiently retrieved without significant loss of DNA. The authors measure the rapid decay of dried DNA at room temperature and present the synthesis of encapsulated DNA in silica nanoparticles as a possible solution. In this form, the protected DNA can be readily applied to digital microfluidics (DMF) used to handle retrieval operations amenable to full automation. A storage architecture is demonstrated, which can increase the storage capacity of today's archival storage systems by more than three orders of magnitude: A DNA library containing 7373 unique sequences is encapsulated and stored under accelerated aging conditions (4 days at 70 °C, 50% RH) corresponding to 116 years at room temperature and the stored information is successfully recovered.

Long-Term Preservation of SARS-CoV-2 RNA in Silk for Downstream RT-PCR Tests

Positive controls made of viral gene components are essential to validate the performance of diagnostic assays for pathogens like severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, most of them are target-specific, limiting their application spectrum when validating assays beyond their specified targets. The use of an inactivated whole-virus RNA reference standard could be ideal, but RNA is a labile molecule that needs cold chain storage and transportation to preserve its integrity and activity. The cold chain process stretches the already dwindling storage capacities, incurs huge costs, and limits the distribution of reference materials to low-resource settings. To circumvent these issues, we developed an inactivated whole-virus SARS-CoV-2 RNA reference standard and studied its stability in silk fibroin matrices, i.e., silk solution (SS) and silk film (SF). Compared to preservation in nuclease-free water (ddH2O) and SS, SF was more stable and could preserve the SARS-CoV-2 RNA reference standard at room temperature for over 21 weeks (∼6 months) as determined by reverse transcription polymerase chain reaction (RT-PCR). The preserved RNA reference standard in SF was able to assess the limits of detection of four commercial SARS-CoV-2 RT-PCR assays. In addition, SF is compatible with RT-PCR reactions and can be used to preserve a reaction-ready primer and probe mix for RT-PCR at ambient temperatures without affecting their activity. Taken together, these results offer extensive flexibility and a simpler mechanism of preserving RNA reference materials for a long time at ambient temperatures of ≥25 °C, with the possibility of eliminating cold chains during storage and transportation.

Scalable Nucleic Acid Storage and Retrieval Using Barcoded Microcapsules

Rapid advances in nucleic acid sequencing and synthesis technologies have spurred a major need to collect, store, and sequence the DNA and RNA from viral, bacterial, and mammalian sources and organisms. However, current approaches to storing nucleic acids rely on a low-temperature environment and require robotics for access, posing challenges for scalable and low-cost nucleic acid storage. Here, we present an alternative method for storing nucleic acids, termed Preservation and Access of Nucleic aciDs using barcOded micRocApsules (PANDORA). Nucleic acids spanning kilobases to gigabases and from different sources, including animals, bacteria, and viruses, are encapsulated into silica microcapsules to protect them from environmental denaturants at room temperature. Molecular barcodes attached to each microcapsule enable sample pooling and subsequent identification and retrieval using fluorescence-activated sorting. We demonstrate quantitative storage and rapid access to targeted nucleic acids from a pool emulating standard retrieval operations implemented in conventional storage systems, including recovery of 100,000-200,000 samples and Boolean logic selection using four unique barcodes. Quantitative polymerase chain reaction and short-read sequencing of the retrieved samples validated the sorting experiments and the integrity of the released nucleic acids. Our proposed approach offers a scalable long-term, room-temperature storage and retrieval of nucleic acids with high sample fidelity.

Structural Dynamics of RNA in the Presence of Choline Amino Acid Based Ionic Liquid: A Spectroscopic and Computational Outlook

Ribonucleic acid (RNA) is exceedingly sensitive to degradation compared to DNA. The current protocol for storage of purified RNA requires freezing conditions below -20 °C. Recent advancements in biological chemistry have identified amino acid-based ionic liquids as suitable preservation media for RNA, even in the presence of degrading enzymes. However, the mechanistic insight into the interaction between ILs and RNA is unclear. To the best of our knowledge, no attempts are made so far to provide a molecular view. This work aims to establish a detailed understanding of how ILs enable structural stability to RNA sourced from Torula yeast. Herein, we manifest the hypothesis of multimodal binding of IL and its minimal perturbation to the macromolecular structure, with several spectroscopic techniques such as time-resolved fluorescence and fluorescence correlation spectroscopy (FCS) aided with molecular dynamics at microsecond time scales. Relevant structural and thermodynamic details from biophysical experiments confirm that even long-term RNA preservation with ILs is a possible alternative devoid of any structural deformation. These results establish a unifying mechanism of how ILs are maintaining conformational integrity and thermal stability. The atomistic insights are transferable for their potential applications in drug delivery and biomaterials by considering the advantages of having maximum structural retention and minimum toxicity.

Bioinspired Cell Silicification: From Extracellular to Intracellular

In nature, biosilicification directs the formation of elaborate amorphous silica exoskeletons that provide diatoms mechanically strong, chemically inert, non-decomposable silica armor conferring chemical and thermal stability as well as resistance to microbial attack, without changing the optical transparency or adversely effecting nutrient and waste exchange required for growth. These extraordinary silica/cell biocomposites have inspired decades of biomimetic research aimed at replication of diatoms' hierarchically organized exoskeletons, immobilization of cells or living organisms within silica matrices and coatings to protect them against harmful external stresses, genetic re-programming of cellular functions by virtue of physico-chemical confinement within silica, cellular integration into devices, and endowment of cells with non-native, abiotic properties through facile silica functionalization. In this Perspective, we focus our discussions on the development and concomitant challenges of bioinspired cell silicification ranging from "cells encapsulated within 3D silica matrices" and "cells encapsulated within 2D silica shells" to extra- and intracellular silica replication, wherein all biomolecular interfaces are encased within nanoscopic layers of amorphous silica. We highlight notable examples of advances in the science and technology of biosilicification and consider challenges to advancing the field, where we propose cellular "mineralization" with arbitrary nanoparticle exoskeletons as a generalizable means to impart limitless abiotic properties and functions to cells, and, based on the interchangeability of water and silicic acid and analogies between amorphous ice and amorphous silica, we consider "freezing" cells within amorphous silica as an alternative to cryo-preservation.

Long-Term Room Temperature Storage of Dry Ribonucleic Acid for Use in RNA-Seq Analysis

RNA is an essential biological material for research in genomics and translational medicine. As such, its storage for biobanking is an important field of study. Traditionally, long-term storage in the cold (generally freezers or liquid nitrogen) is used to maintain high-quality (in terms of quantity and integrity) RNA. Room temperature (RT) preservation provides an alternative to the cold, which is plagued by serious problems (mainly cost and safety), for RNA long-term storage. In this study, we evaluated the performance of several RT storage procedures, including the RNAshell^® from Imagene, where the RNA is dried and kept protected from the atmosphere, and the vacuum drying of RNA with additives such as the Imagene stabilization solution and a home-made trehalose solution. This evaluation was performed through accelerated (equivalent to 10 years for RNAshell) aging and real-time studies (4 years). To check RNA quality and integrity, we used RNA integrity number values and RNA-seq. Our study shows that isolation from atmosphere offers a superior protective effect for RNA storage compared with vacuum drying alone, and demonstrates that RNAshell permits satisfactory RNA quality for long-term RT storage. Thus, the RNA quality could meet the demand of downstream applications such as RNA-seq.

Silica Mineralization of DNA-Inspired 1D and 2D Supramolecular Polymers

The preparation of hybrid materials from supramolecular polymers through the sol‐gel process is presented. Supramolecular polymers are assembled from phosphodiester‐linked pyrene oligomers and act as water‐soluble one‐ or two‐dimensional templates for silicification. The fibrillary and planar morphologies of the assemblies, as well as the excitonic interactions between the chromophores, remain unaffected by the silicification process.

Click and release: fluoride cleavable linker for mild bioorthogonal separation

Herein, we present a water dispersable, magnetic nanoparticle supported "click and release" system. The cleavable linker has been synthesized by using a strain-promoted copper-free "click" reagent to establish the specific link and a fluoride cleavable silane moiety for mild cleavage. Small organic molecules, azide-bearing dyes and functionalized enzymes have been bound to the magnetic particle and released in a bioorthogonal way.

DNA-Based Sensor Particles Enable Measuring Light Intensity in Single Cells

"Lab on a particle" architecture is employed in designing a light nanosensor. Light-sensitive protecting groups are installed on DNA, which is encapsulated in silica particles, qualifying as a self-sufficient light sensor. The nanosensors allow measuring light intensity and duration in very small volumes, such as single cells, and store the irradiation information until readout.

Submicrometer-Sized Thermometer Particles Exploiting Selective Nucleic Acid Stability

Encapsulated nucleic acid selective damage quantification by real-time polymerase chain reaction is used as sensing mechanism to build a novel class of submicrometer size thermometer. Thanks to the high thermal and chemical stability, and the capability of storing the read accumulated thermal history, the sensor overcomes some of current limitations in small scale thermometry.

Silk sericin microcapsules with hydroxyapatite shells: protection and modification of organic microcapsules by biomimetic mineralization

Silk protein sericin based organic–inorganic hybrid microcapsules are fabricated by incubating sericin microcapsules with a supersaturated calcium phosphate solution containing citric acid.

Immobilizing and de-immobilizing enzymes on mesoporous silica

β-Glucosidase was immobilised as a model enzyme within silica mesocellular foam (MCF) at a high loading, further entrapped to achieve higher stability and released unharmed upon need by applying fluoride buffered solutions.